首页|Powerful QTL mapping and favorable allele mining in an all-in-one population:a case study of heading date

Powerful QTL mapping and favorable allele mining in an all-in-one population:a case study of heading date

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The multiparent advanced generation intercross(MAGIC)population is characterized with great potentials in power and resolution of quantitative trait locus(QTL)mapping,but single nucleotide polymorphism(SNP)-based GWAS does not fully reach its potential.In this study,a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice.A total of44 000 genes showed functional polymorphisms among eight parents,including frameshift variations or premature stop codon variations,which provides the potential to map almost all genes of the MAGIC population.Principal component analysis results showed that the MAGIC population had a weak population structure.A high-density bin map of 24 414 bins was constructed.Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development.SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date,including 14 known heading date genes.The mapping resolution of genes is dependent on genetic effects with offset distances of＜55 kb for major effect genes and＜123 kb for moderate effect genes.Four causal variants and noncoding structure variants were identified to be associated with heading date.Three to four types of alleles with strong,intermediate,weak,and no genetic effects were identified from eight parents,providing flexibility for the improvement of rice heading date.In most cases,japonica rice carries weak alleles,and indica rice carries strong alleles and nonfunctional alleles.These results confirm that the MAGIC population provides the exceptional opportunity to detect QTLs,and its use is encouraged for mapping genes and mining favorable alleles for breeding.

MAGIC populationpopulation structurebin mapnovel casual variantsuperior allele

Pengfei Wang、Ying Yang、Daoyang Li、Zhichao Yu、Bo zhang、Xiangchun Zhou、Lizhong Xiong、Jianwei Zhang、Lei Wang、Yongzhong Xing

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National Key Laboratory of Crop Genetic Improvement,Hubei Hongshan Laboratory,Huazhong Agricultural University,Wuhan 430070,China

Institute of Tropical Crop Genetic Resources,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China

Yazhouwan National Laboratory,Sanya 572024,China

National Key Research and Development Program of ChinaSTI2030-Major ProjectsNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaEarmarked Fund for China Agriculture Research SystemNational Key Laboratory of Crop Genetic Improvement Self-Research Program

2023ZD040732022ZD0400131821005U20A203132061143042CARS-01ZW22B0204

2024

10.1093/nsr/nwae222

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ISSN：
年,卷(期)：2024.11(8)